As far as I know it was all done by Minensuchgruppe 1 (Ju 52s with degaussing rings). It had 6 Staffeln which were deployed individually (or split into smaller detachments) wherever they were needed. I've seen references in ULTRA to their working in the Elbe and Gironde Estuaries, in the Aegean and along the Danube.
There's some basic organisational information
here but a quick search suggests most online sources are in German.